1jve
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NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop
OverviewOverview
We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with, nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA x, TTATAATTA, is imbedded in a 27-nucleotide stem-and-loop construct, which, is stabilized by terminal GC base pairs and an extraordinarily stable DNA, loop GAA (Hirao et al., 1994, Nucleic Acids Res. 22, 576-582). The AT-rich, sequence has three repeated TAA x TTA motifs, one in the reverse, orientation. Comparison of the local conformations of the three motifs, shows that the sequence context has a minor effect here: atomic RMSD, between the three TAA x TTA fragments is 0.4-0.5 A, while each fragment is, defined within the RMSD of 0.3-0.4 A. The AT-rich stem also contains a, consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT x, ApA steps have characteristic local conformations, a combination of which, determines a unique sequence-dependent pattern of minor groove width, variation. All three TpA steps are locally bent in the direction, compressing the major groove of DNA. These bends, however, compensate each, other, because of their relative position in the sequence, so that the, overall helical axis is essentially straight.
About this StructureAbout this Structure
1JVE is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
High-resolution NMR structure of an AT-rich DNA sequence., Ulyanov NB, Bauer WR, James TL, J Biomol NMR. 2002 Mar;22(3):265-80. PMID:11991355
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